Parraga-Leo, Antonio; Oskotsky, Tomiko T; Oskotsky, Boris; Wibrand, Camilla; Roldan, Alennie; Tang, Alice S; Ha, Connie WY; Wong, Ronald J; Minot, Samuel S; Andreoletti, Gaia; Kosti, Idit; Theis, Kevin R; Ng, Sherrianne; Lee, Yun S; Diaz-Gimeno, Patricia; Bennett, Phillip R; MacIntyre, David A; Lynch, Susan V; Romero, Roberto; Tarca, Adi L; Stevenson, David K; Aghaeepour, Nima; Golob, Jonathan L; Sirota, Marina

doi:10.1093/jamiaopen/ooae099

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VMAP: Vaginal Microbiome Atlas during Pregnancy

Published Web Location

https://doi.org/10.1093/jamiaopen/ooae099

Abstract

Objectives

To enable interactive visualization of the vaginal microbiome across the pregnancy and facilitate discovery of novel insights and generation of new hypotheses.

Material and methods

Vaginal Microbiome Atlas during Pregnancy (VMAP) was created with R shiny to generate visualizations of structured vaginal microbiome data from multiple studies.

Results

VMAP (http://vmapapp.org) visualizes 3880 vaginal microbiome samples of 1402 pregnant individuals from 11 studies, aggregated via open-source tool MaLiAmPi. Visualized features include diversity measures, VALENCIA community state types, and composition (phylotypes, taxonomy) that can be filtered by various categories.

Discussion

This work represents one of the largest and most geographically diverse aggregations of the vaginal microbiome in pregnancy to date and serves as a user-friendly resource to further analyze vaginal microbiome data and better understand pregnancies and associated outcomes.

Conclusion

VMAP can be obtained from https://github.com/msirota/vmap.git and is currently deployed as an online app for non-R users.

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